Changes
by BBC Addict
Summary: Discovery of Atlantis brings changes to SG-1. Call it head canon. Any drabbles/one-shots here will follow my head canon set forth in the first 'chapter'. These will probably not be in any sort of order. Apologies for any confusing A/Ns-chapters have been moving around from one place to another.
1. Reorganization

Gen. Jack O'Neill sighed as he put the final signatures on orders that would probably change the world. _Of course,_ he thought, _if I stayed home sick one day it might change the world. Or end it._

He threw down his pen. He'd rather face a whole lot of Jaffa than deal with paperwork.

"Walter," he called.

"Sir?"

"Get Major Carter up here."

Minutes later, Sam was knocking on his open door. "Sir?"

"Carter, sit down," Jack instructed as he swung his feet off his desk and assumed a posture more fitting for a general about to handle official business. "Good news or bad new first?"

Sam looked puzzled and slightly concerned. "Um, bad," she replied slowly.

"You're being transferred out of the SGC."

Sam was speechless for a moment. "But, sir-"

"Easy, Carter," Jack said, holding up a hand to forestall her objections. "This leads into the good news. You're getting promoted."

Sam frowned. "What do I care about a promotion? I've been working on the Stargate program for eight years and we would probably all be dead if not for me!"

"Sam," Jack said, hoping to startle her out of tirade by using her first name.

Sam did indeed fall silent.

"Let me explain. You're leaving the SGC but you're not out of the Stargate program. You're being promoted so that you can lead the expedition to Atlantis."

Sam leaned back in her chair, stunned. A moment later, she was playfully frowning at Jack. "You're a jerk, sir."

Jack grinned. "That I am." He pulled a thick file from his desk. "This is just the beginning of all the fun you're going to have," he said as he gave the file a thump before sliding it toward Sam. "My advice is to get a trusty sergeant sidekick, like Walter, ASAP."

Sam grabbed the file. "I think you're right," she replied as she quickly flipped through the pages.

"Look at the bright side, Carter. You'll be in command of Atlantis, I'll be in command of the SGC, we'll both report to General Hammond...and the IOA," Jack added, rolling his eyes.

It only took Sam a second to realize what Jack was saying. "You won't be my C.O. anymore." She smiled, a special smile that she normally reserved for their fishing trips.

"That's right. What's a galaxy compared to Air Force regulations?" Jack quipped.

Sam smiled again, but said nothing. The rest of that conversation could wait until they were off base. "What about SG-1?" she asked.

"SG-1 is officially off-duty for the time being. You and Daniel are going to be busy with official stuff, so new members are being lined up."

"Daniel's going, too?"

"You betcha. Who else is an expert on translating Ancient? Don't say anything, though. I haven't told him he's going yet."

Sam was headed to her office when she bumped into Daniel in the corridor.

"Wow. What's that about?" Daniel asked, gesturing to the thick file in Sam's hands.

"Honestly, I don't know. I haven't really looked at any of it yet." She resumed her walk, calling back over her shoulder, "The general wants to see you." She accompanied the words with a wink that left Daniel puzzled.

Shaking his head, he headed toward Jack's office.

"Jack?"

"Daniel!"

Daniel accepted the unspoken invitation to come in and sit down. "What's up?" he asked.

"What's the one thing you want most?" Jack asked with a sweeping arm motion.

"To stop the Goa'uld from enslaving the universe?"

This was clearly not the answer Jack had been looking for. "OK. What else do you really want?"

"To go a week without risking my life to save the world?"

Jack deflated completely. "Come on, Daniel. Work with me here."

"I'm trying, Jack, but I really have no idea what you want me to say."

Jack took a deep breath. "It starts with At and ends with lantis."

"At...lantis. Atlantis?!" Daniel exclaimed. "Jack! Are you serious? I'm going to Atlantis?"

Jack help up his index finger and Daniel reigned himself in a bit. "You'll be part of the Atlantis expedition, yes. There's a lot to work out still, so you can cool the jets a little."

Daniel started babbling in excitement again before stopping short. "What about SG-1?"

"SG-1 is on stand-down until you and Carter are replaced."

"Why is Sam being replaced?"

"Daniel," Jack said in a tone that clearly indicated Daniel should stop and think it through. "Carter's going to be in command of the Atlantis expedition."

Eventually, Jack managed to get the exuberant archaeologist out of his office. That was two things crossed off his list. He needed coffee.

* * *

The night of Sam's official promotion and reassignment, Sam drove over to Jack's place.

Once inside, Sam felt a little shy and awkward. She'd been here more times than she could count, but this wasn't the isolated cabin in Minnesota. Not having to hide anything had become more uncomfortable than hiding.

Jack came to stand in front on her. "Weird, isn't it?" he said.

Sam grinned and relaxed a little.

Jack smiled. "I don't know what you'd call this thing we've been doing for the last four years, but I do know something else. This is our chance." He reached into his pocket and pulled out a box. "I say we take it, Sam." He flipped it open to reveal a candy ring. "So we can destroy the evidence afterward," he explained.

Sam giggled. "Yes."

Jack cocked an eyebrow.

"I mean yes, sir!"

Jack nodded in approval. "I should warn you, I plan on a very short engagement."

"How short?" Sam asked, slightly concerned.

"Hey, Daniel!" was Jack's reply.

Daniel, Teal'c, and General Hammond appeared.

"Wow. Ok," Sam said with a curt nod.

Jack looked at her, sobering up for a moment. "Really?"

Sam took his hand. "It's definitely not what I ever imagined, but now I can't see us doing anything else."

General Hammond happily performed the ceremony and somehow managed to keep a straight face when Jack pulled out another candy ring, handed it to Sam, and held out his hand expectantly. Daniel, who hadn't known about this part of the plan beforehand, simply rolled his eyes and shrugged. Teal'c looked on stoically, saying to himself that human customs would never make sense.

Once the others had left, Sam and Jack snuggled together on the floor, leaning against the couch.

"I did actually get you something," Jack said eventually. "Not a ring. They're easy to lose and impractical and everyone notices them." He reached into his pocket again and gave Sam a small package. She unwrapped it, curiosity aroused. Inside were two matching bracelets. They looked almost like medical alert bracelets, but instead of big red letters, the plates sported some kind of stone inlay. The stone glowed as Sam picked one up one of the bracelets.

"It's Asgard. It's kind of like those mood ring things, except it doesn't gauge your mood. This glow means you're alive and well. Orange means alive but not well. Red means...bad. No glow..." Jack trailed off. "Gift from Thor. I really do love those guys." Jack clasped Sam's bracelet around her wrist and she did the same for him. "Oh. Did I mention that your bracelet monitors me and mine monitors you?"

"Nice touch."

"Even better, it works long distance. Thor said they have unlimited range. So even if you can't report from Atlantis, when you get there, I'll know whether to be really worried or not."

"What do they do when you're alive and doing really well?" Sam purred.

"Let's find out," Jack said.

* * *

"Unscheduled off-world activation!"

Sirens blared and lights flashed. Jack sighed as he left his desk and jogged down the stairs to the control room. Soldiers poured into the gate room and aimed their weapons as Jack demanded an explanation from the sergeant minding the computer.

"No I.D.C. No teams scheduled to check in." The sergeant paused a moment. "Receiving video transmission."

"Put it through," Jack ordered.

The video feed slowly came up. It was grainy and fuzzy with mildly distorted audio. Jack was very surprised to see who the caller was. "Jonas."

"Colonel O'Neill." There was a hint of relief in Jonas' voice. "I was hoping you'd do me a favor and let me come through."

Jack didn't miss the pleading look in his eyes despite the static in the feed. "Who's your friend?" Jack asked, his intonation on 'friend' indicating his doubt that the man standing in the room with Jonas was actually friendly.

"Otto. He's just making sure I get out of here safely."

"He won't be coming?"

"No, sir. Just me."

Jack nodded to sergeant. "Open the iris." He looked back to Jonas. "All right. Come on down."

Jonas sighed thankfully and made his way to the other side of the room with some difficulty. Jack headed down to the gate and ordered the soldiers to stand down but remain alert. "The second Jonas is through, close it up," Jack instructed.

Moments later, Jonas appeared and Jack stepped up to greet him. "We'll talk later. Infirmary, now."

Jonas protested weakly.

"You're on my base now."

"What happened to General Hammond?"

"He got promoted and I got bumped up a notch on the food chain. Which means you have to do what I say because no one here can countermand my orders. Infirmary. Let's go."

A few hours later, Jack and Jonas sat in Jack's office, waiting for Col. Mitchell. Once he arrived, Jack motioned him to the other empty chair. "Cameron Mitchell, Jonas Quinn." The two men shook hands, Jonas wincing as his arm was jostled. "Ok, Jonas. Care to explain why you showed up here looking like someone used you for a punching bag?"

Jonas sighed. "The Joint Ruling Council fell apart. Then there were power shifts, new people claiming leadership all the time. Finally, the Andari Federation gained control. They've been getting rid of any influential people who are non-Andari. Most of them have never been heard from again. They wanted me to work with them on the naquadria technology, but when I told them I wouldn't work for tyrants and terrorists, they detained me for interrogation and reeducation. I still refused. If Otto hadn't felt guilty about what his bosses were doing and gotten me to the gate, I would have been executed in a few hours."

"No going back this time, eh?"

"No. I guess I'm asking for asylum. Again."

"Want your old room back?" Jack quipped. Jonas shrugged. "What about your old job?"

"But Dr. Jackson's back-"

"There's been a lot of changes since you left. Daniel and Carter are getting ready to head off to Atlantis. Col. Mitchell here is in command of SG-1 and they're short an egghead."

Jonas looked first at Jack and then at Cam. Cam nodded and smiled. "I'd be mighty proud to have you on the team."

"I'd like that very much," Jonas said. Cam slapped him warmly on the shoulder, causing Jonas to grunt and hunch over in pain. "Maybe in a few weeks."

Jack agreed. "In the meantime, you and Lieutenant Hailey can catch up with whatever Carter and Daniel have left unfinished."

Cam frowned. "Homework?"

"I could always assign you to assist Dr. Lee..."

"I'm sure Teal'c and I can find something to keep ourselves busy until Quinn's in shape to ship out."

* * *

**A/N: This doesn't really have a plot. It's more housekeeping/head canon, so I make no guarantees about this continuing any further. I cannot stand Torri Higginson/Dr. Weir so I'm imagining something I'd like better. No Landry, ever. I suppose this does vaguely follow my other Stargate stories where I have Sam/Jack 'date' under the radar. There's not much substantial Sam/Jack until season 4 and Jack is promoted in season 8, so that's what I'm using as a time reference.**


	2. Less Talking

Sam beamed as General Jack O'Neill appeared through the Stargate.

"Carter," he said with a nod and a smile.

"It's great to see you, sir," she said, managing to keep her voice professional. "Sergeant, take the general's things to his quarters," she instructed. The sergeant nodded and complied. "Would you like a tour?" Sam asked Jack.

"That's why I'm here," Jack said, quietly adding, "officially," so that only Sam could hear.

Partway through the tour, alarms began sounding. Sam looked apologetically at Jack and they turned with one accord. They stepped into a transporter only to be joined at the last second by Dr. McKay. Jack rolled his eyes as McKay wedged himself between the pair.

The transporter shuddered and went dark. "Carter?" Jack demanded tersely.

"I don't know, sir. Rodney?"

"Don't look at me!"

"You're the one with the computer in hand, Rodney. Figure out what happened."

"Fine," McKay grumbled. He and Sam awkwardly changed places and he plugged his tablet into the control panel. After a few moments, he launched into an explanation of what was wrong and how it was impossible to fix, but he had an idea.

"McKay!" Jack shouted. "Less talking, more fixing."

Rodney shrank a little, meekly, and miraculously, silently, setting to work.


	3. Selection

Sam was just taking a brief break from studying personnel files when a roving general appeared in the doorway of her office.

"How goes the hunt?" he asked, referring to her current task of selecting her top Air Force candidates for the upcoming Atlantis mission.

Sam frowned. "Actually, sir, I was just about to come find you. I'd appreciate a second opinion. Every single one of these people is qualified for the job. I'm just not seeing anything that makes one stand out more than the others."

Jack nodded and moved toward Sam's desk. "Don't tell Walter I'm in here helping you with your paperwork. I'm dodging quite a bit of my own at the moment."

Sam chuckled. "Your secret is safe with me, as long as no one wanders by the door and sees you in here."

Jack studied Sam's files and agreed that while they were all good candidates, there was nothing outstanding among them. "I've got a file I think you should read. Be right back, unless Walter catches me."

A few minutes later, Jack returned. He handed the file over to Sam. She flipped it open and skimmed the contents. "Are you sure about this, sir? He doesn't have a clean record."

Jack shrugged. "Neither do I." He continued as Sam nodded. "Besides, look at the circumstances of those disciplinary actions. He wasn't leaving anyone behind."

Sam smiled. No man (or woman) left behind had always been a core concept of SG-1 and the SGC. John Sheppard had proved that he felt the same way and that made him stand out more than the other officers in Sam's pile. "I don't know how this recommendation would go over coming from me since he wasn't even on the list," Sam finally said.

"Let me make a call. I'm sure George can pull a string or two."

* * *

**A/N: I'm on a roll with these suckers today! This more or less falls in line with the timeline I set up in my story 'Changes.'**


	4. Welcome to the SGC

Major John Sheppard read his letter with a degree of displeasure. He figured this new assignment was punishment for disobeying orders one too many times and now he was going to be buried beneath a mountain with a bunch of eggheads studying 'deep space radar telemetry' until he rotted or died of boredom.

Doubts notwithstanding, he reported to Cheyenne Mountain at promptly 0800 on Monday the 23. He was escorted to an elevator by a sergeant and they rode down in silence. As John followed the sergeant through a number of corridors, he noticed that there were an awful lot of armed guards. A few minutes later, a team of four soldiers brushed by him in full gear and John noticed strange patches on their arms, a symbol that resembled an upside V with a small circle just above the tip.

The sergeant finally stopped outside an open door and peeked inside. "Major John Sheppard," he announced.

"Thanks, Walter," General Jack O'Neill said. "Major, come join the party."

John stepped into the small office. General O'Neill was leaning back in his chair with his feet propped up on the desk. A blonde woman was seated on the opposite side of the desk with a large stack of files in front of her. "Major Sheppard, Colonel Samantha Carter," the general said, not bothering to change position.

"Colonel."

"Major," the colonel replied, giving him a friendly smile. John began to think maybe this assignment wouldn't be so bad, after all...

"Have a seat, major," the general said, gesturing to the unoccupied chair. John sat. Finally sitting up, the general spoke. "I'm sure I don't have to remind you that everything you see and hear on this base is confidential and not to be spoken of to anyone." John nodded. "You may have figured out that 'deep space radar what-have-you' is just a cover story. What we actually do here is pretty cool." Just then, red lights throughout the complex began flashing and an alarm blared. The colonel and general jumped up as a voice on the intercom cried, "Unscheduled off-world activation!"

General O'Neill and Colonel Carter had left John sitting alone. The general stuck his head back through the door. "Come on, Sheppard. What you're about to see will change your world."

John followed, wondering at the cliché. The trio descended a flight of spiral stairs and entered a small room filled with computer banks. Windows overlooked a large space dominated by a big stone circle with some kind of metal covering the center and a ramp, of all things, leading from the ring to about the center of the room.

"Receiving IDC," a man seated at a computer said. John heard something about okra and irises and as he examined the circular stone, the metal covering slid away revealing a shimmering blue...puddle? It looked like water, but as it didn't come flooding into the room, John had to dismiss that idea. He had to look twice as shapes, no, people, emerged from the blueness. Suddenly he saw Colonel Carter joining the two men and then she gave the older one a hug.

O'Neill called Sheppard after him and headed down another flight of stairs. They passed through an enormous doorway and O'Neill said, "Welcome to the gate room." A few steps further and the general was greeting the new arrivals with handshakes. "Jacob. Martouf. This is Major John Sheppard."

John was about to greet the men when Jacob bowed his head, lifted it again, and spoke in a deep, slightly distorted voice that caused John to step back in alarm. "I'm sorry to cut off pleasantries, general, but we have received some disturbing news about Ba'al."

O'Neill nodded. "My office," he said and Jacob and Martouf headed upstairs. "Not this time, Carter," he said as the colonel made to follow them. She sighed, but didn't object. "Send Col. Mitchell to my office," the general instructed whoever was listening. "Why don't you two go find Daniel? Don't have too much fun," he called over his shoulder as Carter rolled her eyes.

As John accompanied Colonel Carter out of the gate room, he paused momentarily. "I'm confused. What does okra have to do with anything?"

Sam looked at him, puzzled. Then she chuckled. "No, not okra. Tok'ra," she emphasized. "All you really need to know right now is that the Tok'ra are our friends. In fact, Jacob is my dad."

"Has he always been one? With the creepy voice and everything?"

"No," Carter reassured him. "It's been a few years though."

"Daniel doesn't happen to be a Tok'ra, does he?"

The colonel shook her head. "Nope. I was, once, but not for very long."

John took a slight step backward.

Carter shrugged slightly. "Welcome to the SGC."

* * *

**A/N: In keeping with my own personal alternate universe where Sam is in charge of Atlantis, John Sheppard's first look at the Stargate program.**


	5. Dating

SG-1 was returning to the Stargate after scouting the surrounding terrain for any signs of activity. They'd found nothing, as expected. Hailey and Jonas were following Sheppard and Mitchell while Teal'c watched their six. Hailey and Jonas' conversation centered around something math related. Mitchell and Sheppard were swapping stories about women. Mitchell had very few, but Sheppard more than made up for it with many stories about his ex-wife.

"Do you think Colonel Carter's dating anyone?" Sheppard asked, breaking a momentary silence.

Mitchell shrugged as they reached the gate and began retrieving their gear. "I try to avoid digging into the personal life of people who control which planets I'm sent to."

Jonas dialed the gate. Hailey, sending Sheppard a withering glare, stepped through first. Jonas followed. "How does she do that?" Sheppard muttered to himself.

"Do what?" Mitchell asked as he and John climbed the few stairs that led up to the event horizon.

"Look down at me. A girl that small shouldn't be able to do that."

Mitchell shrugged again. "It's a talent, I guess," he said before disappearing into the wormhole.

Sheppard had nearly put his foot through when he felt a heavy hand on his shoulder and he turned to see a somewhat menacing look on the Jaffa's face. "Major Sheppard, if you value your continued existence, you will not pursue Colonel Carter." He released the major but continued to gaze at him.

Sheppard frowned in thought as the larger man disappeared. Teal'c didn't have a thing for the colonel, did he? John shook his head. _Nah_. But somebody else obviously did or Teal'c wouldn't have warned him off like that. It appeared there was a mystery to solve.

* * *

**A/N: In this little scene, Sheppard is temporarily tagging along with SG-1 for a few training missions before he's officially assigned to Atlantis. No, I am not setting up any kind of Sam/John relationship. John's kind of a 'what rules?' guy, so if anyone from Atlantis were to pursue Sam (Rodney excluded, because...eww) I think it would be John.**


	6. For a Price

Jack looked skeptically at Sam. "You're telling me you _want_ McKay?"

"Want isn't the right word. I know he can be incredibly difficult to deal with, but he is brilliant and he's had experience. Since I can't have Hailey, McKay's a good option. Besides, if he's with Atlantis, he won't be here."

"When are you leaving again?" Jack quipped, cheered by the prospect of not having to deal with McKay again. "Maybe we could send him ahead by a few months..."

"No, sir," Sam scolded mildly, grinning.

_Medical team to the gate room! Medical team to the gate room!_

Jack sighed as he stood up. "That'll be SG-14. Grogan probably got shot again."

Sam couldn't help but laugh. "I hope he's all right, sir."

Jack shook his head. "I'm sure he is. I assigned him to SG-14 to minimize the chances of his getting hit. I guess it didn't work." He disappeared down to the control room, leaving Sam studying her lists of candidates for Atlantis. She had interviewed every one personally, though she hadn't chosen each and every member herself. There were really only a handful of people she'd handpicked—the doctors Carson Beckett and Jennifer Keller, and now McKay. She had nixed a few recommendations as well, most notably Peter Kavanagh. He was very intelligent, but he had a real problem working with the military and she wasn't going to have attitudes like that under her command.

"Oh, boy. You've got your angry face on."

Sam snapped out of her reverie. "Don't worry, Jonas, it's not about you."

Jonas smiled widely. "Glad to hear it." He gestured toward the empty chair next to Sam and she nodded, inviting him to join her. "How goes the search?"

Sam nodded. "Pretty good, actually. How are you? I see you got the sling off."

"Yeah. I've just been cleared for active duty."

"That's great. I'm sure Colonel Mitchell will be glad, too. He doesn't really enjoy being stuck here reading mission reports."

"I don't understand why. I've always found them fascinating."

Jack returned, John Sheppard in tow. "Jonas! This is excellent timing. I hear you've been cleared for duty."

"Yes, sir."

Jack pointed at Major Sheppard. "This is Major John Sheppard. He'll be temporarily attached to SG-1. Sheppard, this is Jonas Quinn."

The two men shook hands and the room fell silent. Jack finally clapped his hands together. "Seeing that you're all here with apparently nothing better to do, why don't we all sit down and do some paperwork?"

Sheppard shrunk and mumbled something about having to meet someone before slinking away. Sam shook her head and pointed to her own stack of papers. Jack looked up at Jonas. "Aren't you going to run away?"

Jonas shook his head. "I'm happy to help if you really want me to."

"You see, Jonas, that's why I like you. Always willing to help me out."

"For a price."

"What?" Jack demanded.

"Once we're done, you and me, boxing. It'll be my first time in the ring."

Jack grinned. "You're on."


End file.
